The Kinetics and Thermodynamics of Staphylococcus aureus FabI Inhibition

Integration of drug-target kinetics into the drug discovery cascade requires the ability to rationally optimize the kinetics for drug-target formation and breakdown. This in turn relies upon knowledge of the free energy landscape leading to the final enzyme-inhibitor complex and thus information on not only the ground state structure(s) but also the transition state(s) on the binding reaction coordinate. This chapter demonstrates how detailed mechanistic studies coupled with kinetic methods can reveal the forward and reverse rate constants for enzyme inhibition using staphylococcus aureus (saFabI). It shows that the slow-onset inhibition of this enzyme is in fact due to the need to accumulate enzyme-product complex, and that the slow inhibitor dissociation results from ground state stabilization of the enzyme-inhibitor complex rather than destabilization of the transition state on the reaction coordinate for saFabI. The inhibition mechanisms can vary even between enzyme homologs from different bacterial species.